I thought it would look better to fill the stitch holes from wiring the boat together. So I mixed up some epoxy and wood flour and filled the holes. There is a lot of holes! Its been chilly at night here so the epoxy took a while to cure, I didnt run the heaters much. I did the top half of the boat and 3 days later I sanded all the filler in the holes. Then, I flipped the boat over and did the bottom. Total it took about 7 days and 4 hours of actual work to fill and sand the holes.
You can see the result in the picture below. The dark smudge areas around the filled holes are just epoxy that got down into the wood grain and that will dissapear once the entire boat gets a coat of epoxy. The actual filled holes will likely always be a little off color no matter if you fill them or not. I noticed on other completed kayak pictures that holes that were not filled and just epoxied over got very dark from the end grain showing through the clear coats within the hole, I am hoping the filler helps them to match color a little closer.
With no temps over 50 forecast next week I will just continue sanding and rounding off all the sharp edges to a nice smooth radius. Hopefully the week after this brings a couple days with the temps in the 60's. Otherwise, I might just move the kayak to a location with 24 hour heating so I can fiberglass it. However, that would mean a fair driving distance to work on it but a less dusty, warmer shop where I dont pay the heat bill.